John Patrick O'Neill (February 6, 1952 – September 11, 2001) was a top American anti-terrorism expert, who worked as a special agent and eventually Assistant Director in the Federal Bureau of Investigation until late 2001. In 1995, O'Neill began to intensely study the roots of the 1993 World Trade Center bombing after he assisted in the capture of Ramzi Yousef, who was the leader of that plot.
He subsequently learned of al Qaeda and Osama bin Laden, and investigated the 1996 Khobar Towers bombing in Saudi Arabia and the 2000 USS Cole bombing in Yemen. Partly due to personal friction he had within the FBI and federal government, O'Neill left to become the head of security at the World Trade Center, where he died at age 49 in the September 11, 2001 attacks. In 2002, O'Neill was the subject of a Frontline documentary named "The Man Who Knew."
O'Neill was born in Atlantic City, New Jersey and had a desire to become an FBI special agent from an early age. As a youngster, his favorite television show was The F.B.I., a crime drama based around true cases that the bureau had handled. After graduating from Holy Spirit High School (New Jersey), he went on to college, first attending American University in Washington, DC in 1971. While there, O'Neill also started working at the FBI's Washington headquarters, first as a fingerprint clerk and later as a tour guide. He gained a degree in administration of justice from American University in 1974 and later obtained a Master's degree in forensics from George Washington University.
O'Neill was hired on as an agent at the FBI in 1976. Over the next 15 years, O'Neill worked on issues such as white-collar crime, organized crime, and foreign counterintelligence while based at the Washington bureau. In 1991, O'Neill received an important promotion and was moved to the FBI's Chicago field office where he was assistant special agent in charge. While there, he established the Fugitive Task Force in an effort to promote interagency cooperation and enhance ties between the FBI and local law enforcement. O'Neill also supervised a task force investigating abortion clinic bombings.
Returning to the Washington headquarters in 1995, he became chief of the counterterrorism section. On his first day, he received a call from Richard A. Clarke, who had just learned that Ramzi Yousef had been located in Pakistan. O'Neill worked continuously over the next few days to gather information and coordinate the successful capture and extradition of Yousef. Intrigued by the case, O'Neill continued to study the 1993 bombing Yousef had masterminded and other information about Islamic militants. He was directly involved in the investigation into the 1996 bombing of the Khobar Towers in Saudi Arabia. Frustrated by the level of cooperation from the Saudis, O'Neill purportedly vented to FBI director Louis Freeh, saying that they were "blowing smoke up your ass".
In 1996 and 1997, O'Neill continued to warn of growing threats of terrorism, saying that modern groups are not supported by governments and that there are terrorist cells operating within the United States. He stated that veterans of the insurgency by Afghan rebels against the Soviet Union's invasion had become a major threat. Also in 1997, he moved to the FBI's New York office, where he was one of the agents in charge of counterterrorism and national security.
By 1998, O'Neill had become focused on Osama bin Laden. When his friend Chris Isham, a producer for ABC News, arranged for an interview between bin Laden and correspondent John Miller, Isham and Miller used information put together by O'Neill to formulate the questions. After the interview aired, O'Neill pushed Isham hard to release an unedited version so he could carefully dissect it.
Later that year, two United States embassies were bombed in quick succession in Nairobi, Kenya, and Dar Es Salaam, Tanzania. O'Neill hoped to be involved in the investigation because he had gained a tremendous knowledge of Osama bin Laden's al Qaeda terrorist network. However, turf wars and dislike of O'Neill by some superiors in Washington first meant that the FBI's New York office was left out of the investigation, and later that O'Neill was left behind when other New York–based agents were sent to the region to pick up leads.
O'Neill's rise through the ranks at the bureau began to slow as his personal style chafed others and he made a few slip-ups by losing a bureau cell phone and Palm Pilot, improperly borrowing a car from a safe house, and losing track of a briefcase with sensitive documents for a short period. After being passed over for multiple promotions, O'Neill was pleased to be assigned as commander of the FBI's investigation into the USS Cole bombing in October 2000. However, upon arriving in Yemen, he complained about inadequate security. As his team investigated, O'Neill came into conflict with Barbara Bodine, the U.S. ambassador to Yemen. The two had widely divergent views on how to handle searches of Yemeni property and interviews with citizens and government officials, and they only grew further apart as time progressed.
After a month in Yemen, O'Neill returned to New York 20 pounds (9 kg) lighter than when he left. He hoped to return to that country to continue the investigation, but was blocked by Bodine and others. He continued to investigate the Cole bombing, but eventually decided that the FBI investigation in Yemen must be pulled out due to inadequate security.
A New York Times report of August 19, 2001 suggested that O'Neill had been the subject of an "internal investigation" at the FBI. The report suggested that O'Neill was responsible for losing a briefcase with "highly classified information" in it, containing among other things "a description of every counterespionage and counterterrorism program in New York". The briefcase was recovered shortly after its disappearance. The FBI investigation was reported to have concluded that the suitcase had been snatched by local thieves involved in a series of hotel robberies, and that none of the documents had been removed or even touched.
Several people came to O'Neill's defense, suggesting that he was the subject of a "smear campaign". The Times reported that O'Neill was expected to retire in late August.
O'Neill started his new job at the World Trade Center on August 23, 2001. (Lawrence Wright, The New Yorker, January 14, 2002) He was appointed by Kroll Associates, namely by the managing director Jerome Hauer. In late August, he talked to his friend Chris Isham about the job. Jokingly, Isham said, "At least they're not going to bomb it again," a reference to the 1993 World Trade Center bombing. O'Neill replied, "They’ll probably try to finish the job." 
O'Neill's remains were recovered from the World Trade Center site on September 22, 2001.